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You will have to show them (the court) the documentation and pay stubs for your arguement that is was pay and not a loan. No company would do what they did if it was a loan - they would get you to sign a promissory note or something.
They are lying - do not fall into their trap and somehow agree to repay anything. To the contrary, just read whatever you get and inform them that they are now harassing you about an alleged debt which never was. Continuing their course of action may cause you to take legal action against them. Obviously, your not going to do anything but you don't want to miss something if they file suit in the matter.
They are just throwing stuff on the wall to see what, if anything, sticks!